Using Neural Networks for Relation Extraction from Biomedical Literature

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been proposed to identify relations between concepts in biomedical literature, namely, using neural networks algorithms. The use of multichannel architectures composed of multiple data representations, as in deep neural networks, is leading to state-of-the-art results. The right combination of data representations can eventually lead us to even higher evaluation scores in relation extraction tasks. Thus, biomedical ontologies play a fundamental role by providing semantic and ancestry information about an entity. The incorporation of biomedical ontologies has already been proved to enhance previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1

A Fuzzy Association Rule Mining Expert-Driven (FARME-D) approach to Knowledge Acquisition

Fuzzy Association Rule Mining Expert-Driven (FARME-D) approach to knowledge acquisition is proposed in this paper as a viable solution to the challenges of rule-based unwieldiness and sharp boundary problem in building a fuzzy rule-based expert system. The fuzzy models were based on domain experts’ opinion about the data description. The proposed approach is committed to modelling of a compact Fuzzy Rule-Based Expert Systems. It is also aimed at providing a platform for instant update of the knowledge-base in case new knowledge is discovered. The insight to the new approach strategies and underlining assumptions, the structure of FARME-D and its practical application in medical domain was discussed. Also, the modalities for the validation of the FARME-D approach were discussed

Optical tomography: Image improvement using mixed projection of parallel and fan beam modes

Mixed parallel and fan beam projection is a technique used to increase the quality images. This research focuses on enhancing the image quality in optical tomography. Image quality can be defined by measuring the Peak Signal to Noise Ratio (PSNR) and Normalized Mean Square Error (NMSE) parameters. The findings of this research prove that by combining parallel and fan beam projection, the image quality can be increased by more than 10%in terms of its PSNR value and more than 100% in terms of its NMSE value compared to a single parallel beam

Mining Images in Biomedical Publications: Detection and Analysis of Gel Diagrams

Authors of biomedical publications use gel images to report experimental results such as protein-protein interactions or protein expressions under different conditions. Gel images offer a concise way to communicate such findings, not all of which need to be explicitly discussed in the article text. This fact together with the abundance of gel images and their shared common patterns makes them prime candidates for automated image mining and parsing. We introduce an approach for the detection of gel images, and present a workflow to analyze them. We are able to detect gel segments and panels at high accuracy, and present preliminary results for the identification of gene names in these images. While we cannot provide a complete solution at this point, we present evidence that this kind of image mining is feasible.Comment: arXiv admin note: substantial text overlap with arXiv:1209.148

Chi-square-based scoring function for categorization of MEDLINE citations

Objectives: Text categorization has been used in biomedical informatics for identifying documents containing relevant topics of interest. We developed a simple method that uses a chi-square-based scoring function to determine the likelihood of MEDLINE citations containing genetic relevant topic. Methods: Our procedure requires construction of a genetic and a nongenetic domain document corpus. We used MeSH descriptors assigned to MEDLINE citations for this categorization task. We compared frequencies of MeSH descriptors between two corpora applying chi-square test. A MeSH descriptor was considered to be a positive indicator if its relative observed frequency in the genetic domain corpus was greater than its relative observed frequency in the nongenetic domain corpus. The output of the proposed method is a list of scores for all the citations, with the highest score given to those citations containing MeSH descriptors typical for the genetic domain. Results: Validation was done on a set of 734 manually annotated MEDLINE citations. It achieved predictive accuracy of 0.87 with 0.69 recall and 0.64 precision. We evaluated the method by comparing it to three machine learning algorithms (support vector machines, decision trees, na\"ive Bayes). Although the differences were not statistically significantly different, results showed that our chi-square scoring performs as good as compared machine learning algorithms. Conclusions: We suggest that the chi-square scoring is an effective solution to help categorize MEDLINE citations. The algorithm is implemented in the BITOLA literature-based discovery support system as a preprocessor for gene symbol disambiguation process.Comment: 34 pages, 2 figure